GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Shewanella loihica PV-4

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= uniprot:Q88CC3
         (496 letters)



>FitnessBrowser__PV4:5210745
          Length = 485

 Score =  192 bits (489), Expect = 2e-53
 Identities = 144/462 (31%), Positives = 219/462 (47%), Gaps = 23/462 (4%)

Query: 21  YPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHK 80
           + V  P     IA V      +T   I  A+ A   W    A  R  L+R +  ++ EH+
Sbjct: 27  FDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSANERAALMRKWFNLMMEHQ 86

Query: 81  ADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPL 140
            DLG L+++E GK   E  GE+       D+     +++YG TI +      +     P+
Sbjct: 87  EDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGDTIPAPANDKRILVIKQPV 146

Query: 141 GVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAP 200
           GVV  I+ +NFP A+ A   A AL AG + V +PS  TPL+ALA   L E+A       P
Sbjct: 147 GVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSALAMAELAERA-----GIP 201

Query: 201 AGLAQLVIGGREA--GEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNA 258
           AG+  +V+G      G+ +   P V   + TGST +G+ +  + A    +  +ELGGN  
Sbjct: 202 AGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATSVKKVSMELGGNAP 261

Query: 259 MILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP 318
            I+   AD+D AV+G L S    AGQ C    R+ V + +      +  AA   +++GD 
Sbjct: 262 FIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFTEKFTAAVANLKLGDG 321

Query: 319 RKDNL-VGPLIDKQSFDAMQGALAKARDEGGQ----VFGGE-RQLADQYPNAYYVSPAIA 372
             D + VGP+I K   DA+Q  L    D        V GG+  +L + +     V+    
Sbjct: 322 LGDGVTVGPMISK---DAVQNVLKLVDDTVASGAKLVTGGQPSELGESFLAPVIVTDVTN 378

Query: 373 EMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASG 432
           EMP    + R+E F P+  ++++D   EAL + N+   GL++  +  DI     F+ A G
Sbjct: 379 EMP----LARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDI--GRIFRVAEG 432

Query: 433 SDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474
            + G+  VN G   +     FGG K++G GRE        Y+
Sbjct: 433 LEYGMVGVNEGII-SNAAAPFGGVKQSGNGREGSKYGLDDYL 473


Lambda     K      H
   0.318    0.135    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 536
Number of extensions: 29
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 496
Length of database: 485
Length adjustment: 34
Effective length of query: 462
Effective length of database: 451
Effective search space:   208362
Effective search space used:   208362
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory